In this study, a cleaning scheme based on the combination of bioenzymes and biosurfactants was explored. Morphological and molecular biology identifications were first jointly applied to identify the dominant strains sampled from five ancient books that are stored in the same environment. Cellulolytic experiments were then conducted to evaluate the cellulose degradation ability of the strains according to the cellulolytic digestive index. Finally, paper Mockups for the ancient books were constructed to investigate the most effective combination of bioenzymes and biosurfactants in removing mold stains as well as its effect on the paper’s physical properties. The result concluded that the combination of 3% papain, 7% of sophorolipid or 7% of betaine, and distilled water, achieved optimal stain removal effect with over 50% cleaning rate at 35℃, after 30 minutes of infiltration. At the same time, Sophorolipid and Betaine both have superior deacidification, anti-acidification, anti-aging, and reinforcement capabilities, which can provide extra support to the fibrous structure in addition to cleaning the paper materials. The microbial contamination cleaning agent proposed in this study shows promising application prospects in conserving mold-contaminated paper artifacts.